Reproducibility

• Do everything with code!

  • Helps reduce repetion errors
  • Helps avoid copy/paste barriers
  • Orchestrate workflows

Computational Notebooks

• Authoring environment

  • Code chunks interspersed with natural language
  • aka Literate Coding

• Easy to read and compose

• Graceful degradation

Reports and Expressions

Interactivity and web applications

• Shiny
• Flask
• WebR
• Plotly Dash
• ObjservableJS

Quarto

• Open source / free / portable
• Show explanatory text and code chunks
• Show YAML format option

Quarto Notebook in RStudio

Jupyter Notebooks

Quarto

• A scientific publishing system
• R, Python, ObservableJS
• Compose with standard text editors, or basic IDEs
  • IDEs: RStudio, Jupyter, VSCode

Rendered Outputs

• Artifacts that document a body of work
• Are reproducible and modifiable when data or techniques change
• Easy to update natural language explanations and re-render outputs
• Schedule emails based on report parameters

Summary of benefits

• Using natural language clearly explain data, models, and workflows
• Reduce dependencies on outside and undocumented steps
• Ability to expose technical code chunks depending on audience focus
• State of the art reproducibility
  • 21st century container for evidence-based, computationally-processed research

Definition

• A system to manage projects (repo)
• A system to track how computer files change over time
• A system that support collaborative revision
• More than file synchronization
• Assists in project back-ups

Git

• Free open source
• Wildly successful; most broadly implemented
• In use across the globe
• Use it on any file system
• Track any file
• Use it in any environment

Scalable to project size

Project Repositories

Archival vs version-control

Track change

Branches

GitHub

Git + GitHub

Hubs

• GitHub
• GitLab
• BitBuckent

Duke specific hubs

• gitlab.oit.duke.edu (netId)
• PACE
• Anywhere that data and coding happens.

File Distribution and Collaboration

Other project management features

Basic features

Git features implemented for distribution

• Push
• Public or Private
• Clone / Fork
• Pull Request
• Pull

Push

Clone

Fork / PR

Summary

• Git is used to track changes to your repo
• GitHub is used to distribute your git repo and facility collaboration

Sharing your workspace

Your computation workspace (i.e. your laptop, desktop, cloud credentials)

How

• Binder: package and share reproducible computational environments
  • mybinder.org (public BinderHub portal)
• Zenodo: general, open repository to deposit research papers, data sets, code, reports and related artifacts and connect to a citable DOI.
• Combine GitHub releases with Zenodo to archive your milestones and share the interactive computation in a binder Hub

Binder Hub

• Easiest: mybinder.org open and public
  • quarto use binder
• Security demands may push you to use singularity

Steps

1. Make a GitHub Release at project milestone(s)
2. Connect GitHub to Zenodo
   1. Mint a DOI to a GitHub Release (persistent identifier: citation; milestones)
   2. With DOI, link to ORCID
3. Create a publicly launchable, fully functional computation container of your work

Examples

• https://github.com/libjohn/workshop_rfun_iterate?tab=readme-ov-file#readme
• https://github.com/libjohn/workshop_webscraping?tab=readme-ov-file#readme